Mass Effect 3: The Reaper War
by Tobias5
Summary: Reapers. The greatest threat to life as we know it. It's time we stopped them & all our hopes rest with one man. Shepard. Paragon Shepard for ME1 & ME2. Romance is Liara in both, Wrex lives & the council was saved in ME1. A/U because of Shadow BrokerDLC
1. Chapter 1

**Title: **Mass Effect 3: The Reaper War

**Author:** Tobias

**Rating:** M for Mature

**Shepard Stats:** Paragon Shepard for ME1 & ME2. Romance is Liara T'Soni in both, Wrex lives, and the council was saved in ME1. The rest you'll learn as we go alone.

**Author's Note:** Hello one, hello all! Thank you for stopping by to read this little story of mine! I've had this rattling in my brain since the end of Mass Effect 2. And since all of us are going to wait a year or two for ME3 I thought I might try to tide us over till then. Enjoy my friends, and I welcome any reviews.

**Chapter 1**

"How are we holding up Joker?" John Shepard asked, coming up behind the best pilot he'd ever known, Jeff "Joker" Moreau. Joker sighed and turned the pilot's seat around to face the Spectre. The downcast expression on his face spoke volumes to Shepard.

"We're not so good, Commander." Joker answered. "We can still fly and fight, but until we get the holes in the hull patched over, we can't use the relay to jump back. Emergency containment shields are meant for just that, emergencies."

"I was afraid you were going to say that." Shepard muttered. He sighed and ran hand threw his short brown hair in frustration. "How long until we get the holes sealed for relay jump?"

It was at this moment the hologram to Shepard's left lit up, displaying a blue sphere with a grid on the front. This was the ship's artificial intelligence, EDI (Enhanced Defense Intelligence). Full unlocked and integrated into the ship during the Collector's kidnapping of the crew, she had proven herself to be extremely loyal and helpful during the past few weeks. Shepard may have his own doubts about AI's and their motives, but he did trust EDI completely.

_"Estimates from the repair crews place final repairs around 1700 hours two days from now, Commander. However, these repairs are only temporary. We will need several weeks in dry dock to bring the Normandy back to 100%."_ EDI said in her calm, feminine voice. Shepard swore. He knew the Normandy was in bad shape but he didn't think it was that bad.

"Not as long of a wait I thought it would be." Shepard mused. He scratched his chin for a moment, thinking. "Can we do a couple of relay jumps or do we have to dry dock at Omega? I'd like to avoid being stuck there for a few weeks."

"I think she'll hold up for a few jumps, Commander." Joker replied. "Just don't ask us to fight off the Reaper fleet."

_"Our odds of surviving an assault by the Reaper fleet by ourselves are approximately three hundred billion to one with the Normandy a peak capacity." _EDI chimed in.

"That's a cheery thought, EDI." Joker muttered.

_"Not as cheery as thinking of you crawling threw access ducts. I did like seeing you on your knees, Jeff." _EDI retorted. Both Shepard and Joker stared at the AI. _"That was a joke."_

"EDI," Shepard began, purposely ignoring the creepy feeling he was getting, "send a notice to everyone to gather in the mess at 1800. I want to make an announcement about what we're going to do and where we're going. Tell Sergeant Gardner to prepare for an all hands dinner then too."

"Got a plan in mind, Commander?"

"Yes and no Joker. Yes and no."

* * *

At 1800, Commander Shepard arrived at the mess to see everyone waiting for him as he expected. What he didn't expect was the loud cheer that rang out the minute he turned the corner from the elevator. He waited for the cheer to die down and couldn't help the grin that crept onto his face. He motioned everyone to sit and they all took their places, at the main tables and some extra tables and chairs pulled out for this sit down.

"We have a right to be proud of ourselves." Shepard began. "We completed our mission and saved as many lives as we could, including our own. We all made it back from the Collector's station alive, if a little beat up."

Everyone murmured their agreement and while they did so, Shepard glanced over his team. Miranda seemed to no worse for the wear, as did most of the others. Grunt and Samara were both heavily bandaged, having been with Shepard when they fought the Human Reaper.

"I've also spoken with the Illusive Man. To say he wasn't pleased we destroyed the station was an understatement, but I've done what I said I would, I've stopped the Collectors. I've paid back Cerberus for bringing me back and all they've done. As I told the Illusive Man, I'm cutting my ties with Cerberus." Shepard informed them. He held up a hand to cut off any questions. "Give me a moment to explain."

Shepard took a deep breath before continuing.

"The Normandy has been threw hell and back, as we all have. She needs a few weeks in dry dock at minimum to be back up to snuff. EDI & Joker have informed me that once the hall breeches are closed off we can do a few mass relay jumps. This is good news since we won't have to make port at Omega. I've decided our berth is going to be Illium. It's got resources we need to make repairs, it's safe enough to hire a couple of outside contractors to help speed along repairs, and we can make some coin selling some tech we've come across to fund repairs. Maybe even get even more tech upgrades to better our odds against the Reapers. But most importantly, it's got friendly faces and it's a good place for you choose what you want to do."

"What do you mean, Commander?" Miranda inquired.

"What I mean is I trust you." Shepard said firmly. "All of you."

Threw were a few sideways glances from some of the crew men towards Legion, but the Geth said nothing. It was watching Shepard intently.

"For whatever reason you joined up with me, you became my crew." Shepard said. "I trust all of you with my life and you're just as good as the crew I hand on the SR1, if not better."

Smiles were all around. That was high praise from the Commander.

"But to be honest the direction I'm going to take this crew and ship might not sit well with some of you." Shepard bluntly stated. "Breaking off from Cerberus might already be causing you to question where you fit in here. Simply put, this is my ship. When we make port, Cerberus symbols, markings, and protocols will be out the window. During dry dock I'm going to make contact with Councilor Anderson. He was going to inquire about my status with the Alliance. As you know, I have been reinstated as a Spectre. At the very least this will be a Spectre's ship, answering only to me and the Council. If I have the option and I choose to, I may be reinstated into the Alliance as well. So you may not want to stay. If you don't, I will wish you well, and we will part on the best of terms. If you stay you may have to get used to a few changes, but I want to make this very clear. If you do stay your first allegiance will be to me and our mission to stop the Reapers. So for next few days, I want you to think it over. When we dry dock, we'll be one shore leave for exactly a week before we start repairs and overhaul. I'd like an answer by the end of that week."

The mess had gone quiet by the time Shepard finished his speech. He nodded to them.

"Enjoy dinner, and sleep well tonight. We have a busy couple of days ahead of us. Good night."

Turning swiftly around, Shepard barely made it around the corner before the mess exploded in rush of voices.

* * *

Shepard cupped his hands under the faucet from his sink and splashed it on his face. He scrubbed at his face a bit and reached for a hand towel. After drying his face and tossing the towel into the laundry chute, he stared at his reflection in the mirror. His face and eyes were back to normal thanks to Dr. Chakwas and the medical bay's upgraded equipment. Even the scar from Akuze and the thresher maw attack were gone. His blue eyes were blood shot and heavy bags had appeared under them. He hadn't shaved in a few days and was well on his way to getting a beard like Joker's. Even though it was only 1900 he decided to crash for the night. A deep, long sleep sounded heavenly just about no. Leaving his bathroom, he couldn't help the jaw cracking yawn he emitted. He was just about to pull off his shirt when the door to his cabin beeped, indicating some one outside wanting entrance. Shepard groaned but turned to the door.

"Open." He commanded sourly. The door's holo-panel changed from red to green, and door shot open, allowing Legion the Geth to stride smoothly in.

"Shepard Commander, we wish to speak with you." Legion said in his robotic voice.

"Sure, Legion." Shepard said, a bit puzzled as to why the Geth was here. "Take a seat." He gestured to the couches. Legion eyes them for a moment before choosing a seat far from the Spectre. Shepard sat in his chair for the desk near his bed.

"We wish to have permission to access the FLT communications system. We would like to commune with the collective about recent events and pose an inquiry. We may also wish to converse while linked to the collective on their behalf with Shepard Commander." Legion stated. Shepard was taken back a bit at Legion's request.

"What's this about, Legion?" Shepard asked, curious.

"We wish to inform the collective about all we learned now that we have completed the mission. Then we have a request of a new mission we wish to complete with Shepard Commander's help. Communicating with the collective may take some time however and we know Shepard Commander would wish to monitor us during said time." Legion stated. Shepard frowned but nodded.

"EDI." He called to the control panel by his door. The hologram lit up in response. "Allow Legion extended access to the FTL com system while it's in my quarters."

"_Acknowledged, Commander._" EDI responded. There was a beep and Legion titled his head. _"Legion has accessed the com system."_

"Thank you EDI." Shepard said. He picked up the data pad on the Reaper data EDI had salvaged. He shot one last curious glance at Legion before studying the data again. For the next hour he would glance at Legion, who sat perfectly still on his couch. The Geth's plate on his head would occasionally move but other than a soft hum, Legion did not move or make a sound. Around 2030, Legion's head moved back to its normal position and EDI spoke again.

_"Legion is still connected to the FLT communication system." _EDI called from her terminal.

"Shepard Commander." Legion stated. "We have finished our exchange with the collective. Consensus has been reached on numerous concerns and we wish to speak on behalf of the collective."

"I'm honored to speak with you and them." Shepard said, setting the pad on the table. He figured being diplomatic wouldn't hurt. As far as he knew this was the only time some one had spoken with the collective since the civil war between them and the Quarians. "I hope you don't mind that my ship's AI is recording this conversation.

"We are honored as well, Shepard Commander. We have no objections to the EDI program monitoring our discussion." Legion responded, his voice taking on an echoing quality to it. "We wish to speak with you about the war against old machines and the creators. The mobile platform programs you call Legion have informed us of the events that have taken place shortly before and after its integration into your collective. Your events on the Collector's station are most impressive."

"Thank you." Shepard said humbly. "Legion was an enormous help to the mission. I hope you will allow it to continue to assist me."

"The trust you allow the platform designated Legion are impressive to us, Commander." The Collective said threw Legion. "We even understand restrictions you place upon it given your history with the heretics. However we wish to speak about them and the old machines. We have processes the information on the old machines and their fleet that you allowed Legion to access. We have reached a consensus involving them and the creators. We wish to align ourselves with the collective known as the council and seek peace with the creators."

Shepard stared at the Geth for a long moment in shock.

"This is…unexpected." Shepard finally said.

"Not at all." The Collective responded. "We have analyzed all the available data Legion has collected. We are concerned for the Collective and our survival. Steps are being taken to protect ourselves from heretic infiltrators and the old machine invasion. Also, recent events involving yourself and the creator designated Tali have given us new information as to our creator's race. We have hundreds of colonies on numerous planets and moons in the Perseus Veil. The creator's home world has been abandoned by us for some time, as have most their colonies. We are prepared to reach a peace agreement with them and wish for you to be our representative along with the platform Legion. Given your standing in the creators' eyes we believe you will help us succeed."

"I am honored but I have to ask, how do I know this is not some plan to gain access to the Flotilla or to lure it into a trap?" Shepard asked. Legion was silent for a moment before picking up a blank data pad on the table. The pad clicked on and the screen began to rapidly fill with numbers and statistics. After a few moments Legion set it down.

"We have downloaded detailed information on our numbers, ships, and locations. As you will see Shepard Commander, our numbers alone on mobile platforms outnumber the human species five to one. Our ships also outnumber the Citadel & Alliance fleet as we know it by two to 1. If we wished to annihilate the creators, we would do so. As for learning the locations of the Flotilla, we will not maintain FLT communications to the Legion platform past this meeting. The Legion platform will be willing to be deactivated until it reactivated on the ship to speak with the creator leaders. Then it can be deactivated again until taken far from their location. We have also downloaded this agreement to the data pad with our _signature_ as it were."

Shepard was quiet for a moment, thinking it over. He'd have to talk it over with Tali and contact the Quarian Admirals, but to have the Geth fleet on their side in the war would be a huge asset. Plus the Quarians could go home.

"While the Normandy is being restored I'll try and arrange meetings with the Quarian Admiralty board and the Council. I'll even help to try and convince them to accept but it will be their decision." Shepard answered. Legion nodded and stood. Shepard stood as well.

"We understand Shepard Commander. We have given the Legion platform specs and allowance to share our tech with you for your ship as a gift for your help. We believe humans shake hands to seal a deal?" Legion extended its hand. Shepard gave a grin and shook the Geth's hand.

"I hope this leads to peace between your people and others." Shepard said firmly. Legion nodded.

"As do we Commander. Disengaging link." Legion responded. Shepard released Legion's hand and there was a slight pause.

_"FLT communications link to Legion has been severed. Restoring firewalls and resetting passwords and fail safes."_ EDI called out.

"Thanks EDI." Shepard called out as Legion began to move again.

"Shepard Commander." Legion said in its normal tone of voice. "We thank you for allowing us to speak with you again. We will now return to making repairs on the ship."

"Thank you for giving us this opportunity, Legion." Shepard called after the Geth as it left. Legion did not respond and quickly left the cabin. Shepard sighed and rubbed his eyes feeling more tired then ever.

"It's been a long damn day." Shepard muttered to himself. He glanced at the door before calling out. "Cabin door, lock!"

The door beeped before locking again. Shepard gave a weary sigh before stripping off his shirt and throwing himself onto his bed.

"Lights off!" He called, kicking his shoes off as the cabin went dark.

The next few days were going to be very, very long.

* * *

To be continued…


	2. Chapter 2

**Title: **Mass Effect 3: The Reaper War

**Author:** Tobias

**Rating:** M for Mature

**Shepard Stats:** Paragon Shepard for ME1 & ME2. Romance is Liara T'Soni in both, Wrex lives, and the council was saved in ME1. The rest you'll learn as we go alone.

**Author's Note:** To be honest I didn't expect as much of a response that I got! I couldn't believe how many reviews and story alerts I saw for this fic in just two weeks! Thanks you guys and I hope this chapter is as good as you hope for. Review responses are at the end of the chapter.

And if you want to know where I got all my info check out the ME wiki, just take out the spaces: http:/ masseffect. Wikia. com/ wiki/ Mass_ Effect_ Wiki

It's a life saver, helps me keep everything straight.

**Chapter 2**

Shepard was right. The next few days were long. From 600 hours to 2300 hours, the entire crew worked themselves to the bone. Everyone pitches in where they could, even the squad members who had no idea how to tell the difference between comm cables and life support lines. Still the extra muscle was appreciated, especially Grunt's, who had taken it upon himself to lug the replacement panels for the hull single handedly, earning much gratitude from the exhausted repair crews. Legion itself did not stop, moving from one job to the next. Unlike the others he did not need breaks or time sleep and moved from one task to the next at a maddening pace. What surprised Shepard the most about it was that Tali was often seen working with the Geth. EDI kept a close on them on Shepard's orders but had nothing negative to report. On the contrary she said the duo had managed to increase engine efficiency by 13%, a remarkable feet. Zaeed, Jack, Garrus, and Thane were repairing the guns. Garrus's upgrades had done their job beautifully but had the un-anticipated side affect of sending a power surge back into the system after shut down. They could still be used but if they were shut down again it would have burnt out power systems for the entire deck. The four of them were installing surge protectors and buffers, and replacing burnt wires. A temporary measure until they could dry dock and give the guns a complete overhaul and upgrade the wiring system. Samara was helping Mordin and Dr. Chakwas with the few injured they had and the rare crew member who pushed themselves to breaking and ended up collapsing. Miranda & Jacob had taken it upon themselves to focus on restoring primary power to most of the ship. Shepard had to do a double take when he was checking on the repairs on the cargo bay to find Miranda in a pair of dirty coveralls with dirt and greased smeared all over her. He discretely snapped a photo of her and stored it with the others.

It was a habit he'd developed after Akuze. After losing those crew members, he'd been uneasy as the memories of their faces only came to him from the night of the slaughter. The wife of Private Johnson had given Shepard a picture of him and Shepard the night they had gone out to celebrate the birth of the Private's daughter as a memento Shepard had grasped onto the idea immediately and asked the family members of the other squad members for a photo. He now had a digital album store with a photo of each crew member he had ever served with. The picture he had framed of Liara was taken from that album. Shepard smiled to himself as he finished his morning coffee Repairs had been completed and it was time to see how well they had put the Normandy back together. He left his cabin, still clutching his coffee mug tightly to ward off the deep ache he felt from the past few days of hard labor and repairs. He sipped his coffee and rode the elevator in peace, stepping out into the busy hustle of the CIC. Checking his terminal for any messages and finding none, Shepard check in with Kelly.

"Everything squared away for this morning Kelly?" Shepard inquired. The chipper redhead nodded.

"Yes sir! Joker reports that everything is ready for Mass Relay jump." Kelly reported. She glanced around a bit before speaking again. "Though the crew is a bit nervous about repairs holding up." That was obvious to Shepard. The whole bridge crew, while busy, seemed tense. Everyone was checking, then re-checking, and checking again to make sure everything was ready.

"I'll speak to them after I speak with Joker and EDI." Shepard remarked. He strode away finishing his coffee. He stopped a crew man who was taking a trey of empty coffee mugs to the galley to add his and headed for Joker. The ace pilot was already working away, checking his own readings and then doing the scans again.

"We all set, Joker?" Shepard asked. Joker didn't even bother turning around but Shepard could hear the grin in his voice.

"As we can be, Commander." Joker replied. "We'll know for sure when I gun the throttle to see if we blow up or not."

_"Our odds of death upon tripping the relay are one in two million, Jeff." _EDI pipe up from next to Joker.

"That's a comforting thought." Joker muttered. Shepard shook his head in amusement.

"Patch me into the ship comms, EDI and signal pre-FTL travel warnings." Shepard ordered.

_"Comms are open and pre-faster than light warnings are initiated"_ EDI replied. Shepard took a small breath before speaking.

"As I'm sure you noticed, we're about to make our relay jump sequence." Shepard said to the crew. "I know some of you are nervous, maybe even scared if our repairs will hold for the jump. I'd like to think I've come to know this crew well over the past month. You have done outstanding work in the past and these past few days are no exception. So assume your initial FTL stations and let's go home." He motioned to EDI to cut the comm and it clicked off.

"Hit it Joker and take us home." Shepard ordered. Joker grinned and shot the Commander a thumbs up.

"Here we go sir, hold onto your shorts and don't stain'em." Joker said, keying in the sequence. The Normandy shook slightly before the relay triggered and shot the ship to it's destination.

* * *

After a gut wrenching trip that took half the day, the Normandy emerged in the Tasale system. Shepard breathed a small sigh a relief as he looked out the froward windows and spotted Illium in the distance.

_"My apologies Commander." _EDI spoke. _"I should have anticipated that the Normandy would shake during FTL travel. The replacement panels are adequate but we do not have the equipment to align the perfectly so they resonated slightly out tune with the rest of the ship during the jump sequence."_

"It's alright EDI, we made it in one piece and safe and sound. That's what matters." Shepard said, and turned to Joker. "Set course for Illium and inquire about a long term dry dock, hopefully near where our last one was."

"Aye, aye Commander." Joker said, setting course. He shot a smirk over his shoulder at the Commander. "Would you like me to let Liara know we'll be there soon?"

Shepard felt his heart quicken at the thought.

"Yes, give her a heads up. We may need her help securing supplies and reliable repair crews." Shepard said after a moment, and turned to head for his cabin.

"Whatever you say, Commander." Joker muttered, grinning to himself.

* * *

As luck would have it, there was a dry dock bay next to the main docking platform they had used last time. It meant a bit of a longer walk but not by much. They spent about an hour hovering in front of the door as the Asari who owned the bay confirmed Shepard's identity and credit. Councilor Anderson had been good on his word and Shepard found his civilian accounts had been restored, so her had no problem putting a down payment on the bay. When he contacted the Council and informed them of the past few days he hoped he could get them to foot the rest of the bill for the bay and repairs.

After they finally docked most of the crew was assembled on the CIC in their civilian clothes. Shepard was pleased to note that none of them had data pads handy to hand him their resignations. Hopefully they would all come back after shore leave. As the docking doors opened Shepard turned to them with a grin.

"Crew dismissed!" He barked and the crew broken into cheers. They began hurrying past him, most wishing him well and to have a good week. He did notice the only people from his squad in line were Grunt, Zaeed, Jacob, and Samara. He watched them curiously as they approached, last in line. Zaeed approached him first.

"Well Shepard." Zaeed said in his gruff voice. He had a large duffel slung over his shoulder and large bag by his side. "I've got some things to take care of and need to put my feelers out for Vido, _again_."

"I'm sorry to see you go, Zaeed." Shepard said quietly. Zaeed shrugged.

"You've got enough muscle on this ship and I fulfilled my contract. You didn't die, and I confirmed the other half of my pay as we landed. It's already been deposited so I'm done with you." Zaeed grunted. Shepard stared at Zaeed for a moment.

"The Illusive Man hired to make sure I didn't die?" Shepard said incredulously.

"That and help you kill some Collectors." Zaeed retorted, and picked up the large bag with his free hand. "I've got shit to do now, so I'll be on my merry way. I left my contact info in the computer, so if you can pay and need my help, give me a holler. Or don't, I don't give a damn." Shepard watched in bemusement as Zaeed strolled out.

"Friendly guy." Shepard muttered. He turned his attention back to Grunt, Jacob and Samara. Grunt stepped forward quickly.

"Just going to pick up some supplies, maybe some Krogan ale. Want some Shepard?" Grunt demanded. Shepard shook his head with a laugh, and Grunt stomped his way to the exit. Samara and Jacob exchanged a look. Samara motioned Jacob to go first and Jacob nodded her thanks. He handed Shepard a data pad, and Shepard gave another sigh as he saw it was a letter of resignation.

"You too, Jacob?" Shepard stated. Jacob nodded. "Care to explain why? You're a good man and I could really use you."

"Commander, with all due respect I simply do not agree with your decision to leave Cerberus. I may not like the Illusive Man's methods some of the time, but he gets the job done without the bureaucratic red tape. Now after everything we've done, you're rushing back to that political shit storm." Jacob said angrily. "No sir, I can not remain aboard a ship run by the Council or the Alliance."

"If that's your decision, I won't stop you." Shepard said. When Jacob gave him a salute, Shepard returned it. "Good luck, Jacob."

"Same to you Commander." Jacob said. He picked up his duffel and headed out. Shepard sighed and turned to Samara who was watching with an amused expression.

"I hope you haven't come to tell me your oath as well." Shepard quipped. Samara gave a small laugh.

"I did Shepard. In fact my oath expired the moment the Collectors were wiped out." Samara said. "I did come here to ask if you would mind having me swear another to you and your cause with the Reapers?"

"I'd be honored." Shepard replied. Samara knelt before Shepard and quietly spoke her new oath.

"By the code I will serve you Shepard. Your choices are my choices, your morals are my morals. Your wishes are my code." Samara swore. As before a biotic field flared around the Asari Justicar. Samara rose to her feet and smiled. "I do know you will not make me do anything dishonorable after spending time with you. I was wondering if I might accompany you ashore? I would like to meet this Liara of yours."

"I'd welcome the company." Shepard replied.

* * *

The walk to Liara's office was pleasantly quiet. Samara did not speak much, merely walked next to Shepard, keeping her eyes alert for any danger. Shepard was in his armor, died dark black with dark blue highlights. He found it served him best, especially with the modifications for extra ammo clips on his left arm and belt, and the extra shield generators in the back plating. He also preferred to go without a helmet, it was easier to see in wider range. As they headed up the stairs to her office, Shepard blinked. Liara had replaced the traitorous Nyexeris with a male Turian. He was not dressed in business suit but with full armor and a machine gun within reach on the desk.

"Welcome Commander Shepard, I'll let Miss T'Soni know you're here." The turian greeted them. He pressed the intercom on the desk. "Ms. T'Soni, Commander Shepard is here with an Asari Justicar."

"Let them in, Kurus." Liara replied softly. The turian, Kurus, let go of the intercom and pressed a switch next to it. The office doors opened with a click.

"Thanks." Shepard said to the Turian. He had a bad feeling about this, Kurus seemed very tense. He strolled in and noted Liara had re-arranged her office a bit. Her desk was now off to the right, her back against the wall and facing the windows.

"Shepard, it's good to see you again." Liara said. Shepard smiled at her and moved towards her, coming around her desk.

"Liara. It's good to see you again, too." He said, approaching her. Liara eyed him warily.

"Shepard what are yo-mmph?" Shepard cut Liara off as he kissed her. Liara was surprised but then leaned into the kiss. Samara turned her back and studied the view out the windows to give them a moment of privacy. After a few minutes the kiss broke.

"I missed you." Shepard whispered to her. Liara blinked and gave a small smile, visibly relaxing.

"And I missed you as well." Liara responded. "I'm sorry, things have been tense lately."

"How so?" Shepard asked, moving back and sitting on the edge of Liara's desk. Liara sighed.

"I was combing threw Nyexeris's data when I discovered something incredible. As the Observer she had done something no one I knew of had. She had met the Shadow Broker face to face." Liara said triumphantly Shepard's eyes grew wide and he smirked.

"Congrats." Shepard said. "Did she record where and when?"

"Better." Liara said, smiling. "She recorded the actual meeting itself."

"She _recorded_ a meeting with the Shadow Broker?" he said incredulously. Liara nodded.

"Yes as protection in case he decided she was expendable, according to her notes. It took place the night before you helped me expose her and according her notes he wasn't planning to leave for a month. I've used every resource I had at my disposal, every favor I collected, and promised dozens of others. I confirmed it Shepard, and this is the Shadow Broker." Liara leaned forward, typing into her computer. Samara came away from the windows, curious to see the Shadow Broker as well. Liara opened a few files before selecting a recording of a security feed. They watched it play, Nyexeris waiting in the shadows of an alley. A bout two minutes later an Elcor came strolling into the alley. Shepard thought he must have been the Shadow Broker's bodyguard before he spoke.

_"Pleased: You have done well so far Nyexeris. I have learned that Shepard will be arriving on Illium soon. You will observe his interactions with T'Soni carefully. You will confirm if he is indeed her mate."_

_"I live to serve Lord Shadow Broker."_

_"Smugness: Yes I know you do."_

"The Shadow Broker is an _Elcor?_" Shepard exclaimed. Liara stopped the video.

"I was shocked myself, but I have confirmed it. His real name Xelrot and he's a former Elcor Elder. Nearing the end of his life, he's 437 years old. Apparently he started when he was very young." Liara informed them and then grinned wickedly. "I distributed his identity over the inter-world core text. The Council and hundred of other mercenary groups have been informed. Illium is in locked down and have his ID. He's currently trapped on planet while some mercs I have hired are trying to track him down. I have single handedly brought his network down!" Liara exclaimed Shepard couldn't help but grin.

"Good for you Liara." he said. He nodded tot he new layout of the office. "Is this why you redecorated? Protection for when you capture him and have him brought here?" Liara winced.

"Not exactly Shepard." Liara muttered. "I got word shortly after I went public with his identity He's put a hit out on me." Shepard stared at her, before frowning.

"You can come stay with me on the Normandy, Liara. We're dry docked for repairs, and I can't think of any place safer." Liara smiled and took his right hand in hers.

"I'd like that Shepard, and after, when I finally get him perhaps you can make room for me again?" Liara asked. Shepard smiled.

"I'll always have room for you Liara." He said to her. Samara turned away to give them a moment again. She frowned as she looked out the window. Something had caught her eye in the distance.

"Shepard, I see something out there." Samara responded. Shepard turned away from Liara, motioning for her to stay at her desk.

"That glass is built proof with kinetic shielding I had installed yesterday." Liara said from behind them as they approached the large window. Shepard frowned, looking.

"Where did you see it?" he asked. Samara nodded to the left by a walkway corner one floor above theirs

"By the corner." she said, frowning. Shepard stared for a moment, he saw nothing. He was about to respond when he saw it. A cloaked shape shifted on the corner.

"I think we need to leave." Shepard said, turning back to face Liara. He felt a cold chill settle in as he looked at her.

"What?" Liara asked, unaware of the small red dot that had appeared between her eyes.

"LIARA GET DOWN!"

The window's kinetic barriers shattered and the window cracked as a bullet punched threw.

Liara screamed.

* * *

To be continued…

* * *

A/N: HA! I love cliff hangers! Don't you guys?

Review responses:

Domnu Edoc'sil: I'm glad you don't see where it's going! That'd take the fun out of it! Enjoy!

MasterYuri666: Glad to see you're liking it! I really enjoy a good femShep story as well. Have you read anything by Prioris? She writes a damn fine story and they're femShep centric too.

outlaw hunter: Isn't it nice to see some one who thinks like you so much? *grins* Enjoy!

JsaysNo: I always thought they put Legion in far too late myself. There's so much you can explore with a Geth character.

Flamehead23a: Thanks and enjoy!

Bandgsecurtiyaw: Thank you! Enjoy!

Pico: Ah now this is tricky to answer. I was going to reveal some as we went along but I will answer what I can.

Yes I did save the Rachni Queen. No Wrex wasn't there. As for any possible Rachni interactions I'm not saying! *grins happily* More to come on that!

As for the genophage cure I did save it. Will it have any baring on the story? Maybe, maybe not. Wait and see.

As for who died I can answer that whole heartedly. Ashley died, as she should have. I hated her character. I always have and I always will. Why you may ask? Don't get either your paragon or renegade maxed before you have to talk on Virmire in ME1. Then you'll see why I hate Ashely.

As for how I did loyalty missions for the team members I focused on what I wanted down the road. So I acted accordingly and treated them okay.

As for the Liara and Shadow Broker thing, you're getting your answer to that now aren't you? *cheeky smile*

Yes I saved the entire Normandy crew. As for the old crew? Wait and see...

Okay folks that's it for now! Look for an update in a couple of weeks! I'll try to keep to about a two week schedule but no promises.

See you later folks!

~Toby


	3. Chapter 3

**Title: **Mass Effect 3: The Reaper War

**Author:** Tobias

**Rating:** M for Mature

**Shepard Stats:** Paragon Shepard for ME1 & ME2. Romance is Liara T'Soni in both, Wrex lives, and the council was saved in ME1. The rest you'll learn as we go along.

**Author's Note:** Well, I hope the threats against my life and manhood will stop now that the wait is over. And fyi for the future, I love cliff hangers. *grins*

**Chapter 3**

Shepard dove for Liara as she was thrown back against the wall. Her beautiful blue eyes were wide in shock as her hands clutched at her stomach, dark blue blood running from her fingers. She slid down the wall, raising her head to stare numbly at Shepard as she fell down behind her desk. Shepard practically dove over the desk to land at Liara's side, grabbing his medi-gel. Samara dove to the side, her biotic shields flaring into existence

"It's going to be okay." Shepard said. Liara stared blankly at him, as he pried her hands away. Shepard felt his heart drop at the sight of the large hole in Liara's stomach. He worked frantically, ignoring the sound of the office door opening. Kurus charged in, his assault rifle at the ready.

"Ms. T'Soni are you-?" Kurus was cut off as the windows were shattered under a hail of gunfire. Shepard was only vaguely aware of this happening, trying to force as much medi-gel into the wound as possible. Liara seemed to out of her daze to scream in agony. She clawed at her stomach above the wound.

"Something is digging into me!" Liara screamed. Shepard stopped, trying to think what to do. The Samara was next to them, glowing with her biotic powers.

"It's a burrower round." Samara said shortly, she gave Shepard a sad look. "They cut and dig until they reach the victim's brain. This assassin knows what they're doing, Shepard. They shot her directly in her brachial heart, she's bleeding out."

"We need to get her back to the ship." Shepard said. He tried to poke his head over the desk but gunfire caused him to duck back down. He reach up to his comm ear piece and signaled the ship. "This is Shepard, EDI is Doctor Chakwas still there?"

_"Yes, Commander."_ EDI responded. _"She was preparing to depart shortly however."_

"EDI signal a code Red medical emergency! Samara is bring Liara T'Soni in with a severe gun shot wound and burrower round in her!"

"_Acknowledged Commander."_

"I'm going to bring her?" Samara questioned. Shepard nodded and primed the only two grenades he carried, in his left hand. The grenades were meant to signal in case he needed a pick up in an area where his comms were jammed and gave off colored smoke.

"When the room is filled with smoke from these signal grenades, take her and move as fast as you can for the Normandy while I draw the assassin's attention." Shepard said. He grabbed his pistol with his right hand. "Maybe I can even catch him."

"Shepard, no-!" Liara tried to speak but began to give a deep, wet cough. Shepard felt a cold sensation run up his spine as he saw blood speckling her lips. His eyes narrowed as he readied the grenades.

"You ready, Samara?" Shepard demanded. Samara nodded and moved next to Liara.

"Ready, Commander." Samara said and Shepard lobbed the grenades over the desk. They went off, filling the office with thick red smoke.

* * *

Actus growled to himself. The entire office was filled with red smoke and he couldn't see anything. He was half tempted to switch back to his assault rifle but he had burned threw his thermal clip. It would take far too many precious moments to switch it out and he couldn't risk them running for cover while he did so. He had his rifle though and it had fourteen burrower rounds left plus the thermal clip itself for normal rounds. He was just debating changing position to get a better angle on the office, maybe even find a way to get a lock on threw the smoke, when some one burst out of the window from the billowing smoke. It was Shepard, the human Spectre.

Actus grinned. Shepard was his second target. The Shadow Broker knew the human had helped this Asari bitch track him down and even helped get the Overseer killed. His orders hand been clear, wait until the Spectre arrived to see T'Soni and kill them both. Actus sighted the human, but he was moving in zig-zag pattern, it made his difficult to track. Actus blinked as the human raised a pistol in his right hand in his direction. What was that human doing now?

Actus got his answer as the Spectre fired a few shots. He felt them bounce off his shields, much to his horror. They had spotted him before he took the shot and those rounds and destabilized his camouflage Actus growled, weighing his options. He heard shouts of surprise as he was revealed. He was a couple of floors above the human the angle would soon be wrong for the human to be able to hit him if he kept running at him. He decided he'd retreat for now and finish off the human later. Word was it that the human's ship was dry docked for repairs anyway. Maybe he could sneak in with the repair crews and blend in? Actus was sure humans couldn't tell one Turian from another. Actus was just about to shoulder his rifle when the human slammed his pistol to his leg. Actus's eyes widened as the human drew a large rocket launcher from his back. Surely the human wasn't going to-

Actus let out a very un-Turian like scream as the human fired.

* * *

Shepard felt cold rage filling him as he fired the M-920 Cain at the floors above him. He was relatively most of the bystanders had fled when the assassin was revealed but he wasn't even concerned with that. All he wanted to do was bring this assassin down to his knees and press the foot of his boot on his throat until his mandibles twitched in agony. He had dared shoot some one Shepard cared about and there would be _hell_ to pay. The Cain round impacted with the concrete walkway, almost vaporizing the walkway above him. The explosion collapsed the section above the one it hit and sending large gouges on the one Shepard stood upon. The walkway came crashing down revealing the only one upon it was the Turian assassin Shepard got a better look at him. He was wearing all black armor and had dark grey skin. Judging by the expression on his face and the way his mandibles were spread, the assassin was surprised to still be alive. He wasted no time in trying to stay that way, however. He jerked his rifle up, firing at Shepard. Remembering how easily those rounds had torn threw the reinforced shields on Liara's office window, Shepard dove to the left behind some rubble. The assassin stopped firing long enough to climb over the skid and jump off. Swearing, Shepard ran to the side and watched the Turian snatch onto the ledge a floor below and pull himself up. Shepard snarled and took a deep breath before jumping over the side.

* * *

As soon as Actus pulled himself over the ledge, he collapsed onto his butt. He leaned back against the concrete barrier catching his breath. That damned, crazy human had vaporized part of the city just to get at him. It was an incredibly bold move, one worthy of a Turian. He was just about to force himself back to his feet and get the hell out of here when he heard a woman scream above him. He looked up, his mandible dropping yet again in shock. The fool Spectre had thrown himself off to follow Actus! Watched in horror as the human grabbed the railing just as Actus had.

"Shit!" Actus shouted. Panic was gripping his heart as he turned to flee. This human was unshakable! Actus shoulder his sniper rifle, breaking into a full fledged run. He had to get off world and fast! He turned left to cut threw the market to get to his shuttle. Once there he'd haul ass for the cargo docks and get on the soonest transport off world. Screw the money!

* * *

Shepard's left arm felt like it was dislocated or damn near close enough to hurt like it was. Shepard grunted and swung his right up to grip the rail. He pulled himself up, the ribs on his left side aching from where he had slammed into the walkway. He pulled himself onto the walkway just in time to see the assassin running into the market. Shepard uttered a small growl as he got over the rail. He broke into a hard run, ignoring the pain in his body and the small whine and click he heard emanating from his left side. He ignored everything but the Turian. The market was crowed today, and they were both shoving shoppers and attendants out of the way. The Turian had a hell of a lead on him and sirens were starting to go off. Shepard was worried that the assassin would get away when a Krogan in black and orange armor seemed to come from nowhere. He slammed a huge crate into the assassin's face, knocking him to the ground. The assassin hit the ground, out cold. Shepard came to halt not far from Grunt and the assassin

"Krogan ale, Shepard." Grunt said, gesturing with the crate in his arms. "It's used for more than just drinking."

"Thanks for the help, Grunt." Shepard said, securing the Turian's hands and then stripping him of his weapons. He handed those to Grunt who took them without complaint. Shepard picked up the Turian and slung him over his right shoulder with a grunt. "I need to get back to the ship, you mind coming with me?"

"Only if you promise to let me torture that Turian for a bit." Grunt grumbled. Shepard couldn't help smiling a bit.

"If he proves stubborn when I ask him a few questions I'll let you have a crack at him but let's see what Garrus and Jack can do with him, alright?"

"Very well..."

* * *

They got back to the ship just as Garrus, Jack, and Miranda were leaving fully armed to find Shepard. They blinked in surprise as the Normandy's doors opened to reveal Shepard with Grunt and an unconscious Turian over one shoulder.

"Shepard!" Garrus exclaimed in surprise. "Samara told us what happened and we were coming to help..." Garrus trailed off as Shepard limped in. Miranda frowned when he walked past her, the click and left side were making were starting to get louder.

"It sounds like you might have over extended some of the servos in your left arm and leg." Miranda noted. "I think we need to go to medical and have you checked over."

"I'm heading there right after I drop our guest in Zaeed's old room." Shepard said wearily. Now that the adrenalin was wearing off, he was starting to feel everything he had done.

"I'll take him there, Shepard." Garrus offered. Shepard shrugged and dumped the assassin to the ground. The assassin moaned but Jack silenced him with a solid kick to the side. She grinned evilly.

"Do we get to have some fun with him?" she asked coyly. Shepard nodded, much to her delight.

"Find out what he knows." Shepard ordered as Garrus picked up the assassin "I want to know who hired him and most importantly, if it was the Shadow Broker who did, where is he."

"Sure thing, Commander." Garrus said, heading off for the elevator, Jack following with an eager smirk on her face. Grunt nodded to Shepard before going with them to stare his ale in his room. Shepard took a deep breath and headed for the elevator. He turned to Miranda who was walking with him. "How's Liara?"

"Dr. Chakwas was working on her with Samara's help when I left to get Garrus and Jack." Miranda said, studying him with a frown. "You must have hit something very hard to do any kind of damage to the servos."

"Nothing we didn't encounter with the Collectors." Shepard said. He waited for the elevator to return.

"Which just took place less than a week ago. The servos may be composed of nanites but they still draw their base materials from you Shepard. You need to rest." Miranda scolded. The elevator arrived with a ding and the doors slid open. They stepped on. "I think I should give you a look over with a hand scanner from my quarters."

"Fine, but I'll be waiting outside medical." Shepard responded, hitting the level he wanted. The wait was agonizing, and when the doors finally opened Shepard didn't even wait for Miranda. He moved to the windows of the medical bay and started in. Samara and Dr. Chakwas were in scrubs and working on Liara. Shepard raised his right arm up and placed it on the glass, leaning against it. His whole body was aching and the ribs on his left side were throbbing steadily, as was his left shoulder, elbow and knee. He felt weak as he watched Liara's sleeping face and the monitors in the room. He ignored Miranda as she came up behind him and began scanning him. She scanned his thoroughly for a solid half hour. Shepard didn't move, watching and waiting. During that time he saw them remove a bullet from Liara's body that had a small set of blades and claws with a glowing red tip. He let out a sigh of relief, that must have been the burrower round.

"You have three broken ribs, a partially dislocated shoulder, a fractured elbow and you crushed some servos in your knee, all on the left side." Miranda said in exasperation. "It's like you fell off a building and landed your left."

"Not far from the truth." Shepard muttered and Miranda sighed behind him.

"As soon as we can I'm going to have to examine you and possibly put you under to replace those servos if the nanites can't restore them." Miranda scolded as Shepard waited.

"Later." Shepard said absently, watching the Justicar and Doctor work on the woman he loved.

Miranda shook her head and walked off, muttering something about men under her breath.

* * *

Four hours later, some one shook Shepard awake. He had pulled one of the mess chairs to the window to watch and wait. He must have fallen asleep. He blinked and looked up, seeing an exhausted Dr. Chakwas standing there. She smiled gently at him.

"She's going to be okay, Samara got her here quickly and was a great help in locating the burrower. I was even able to repair the damage to Liara's brachial heart. She's going to be bedridden for a month but she'll be okay." Dr. Chakwas said. Shepard stood, wincing as his left side protested at the movement. He looked in and saw Liara was sleeping deeply.

"Can I go in?" Shepard asked. Dr. Chakwas nodded.

"I gave her a strong sedative, she'll be asleep till at least tomorrow morning." she replied. Shepard nodded.

"Thanks Doc." he said, moving past her. Dr. Chakwas shook her head as she watched him limp in. He sat in a chair by her bed and took Liara's hand in both of his.

"I'll have to look him over in the morning." the doctor muttered to herself and yawned widely. "But first I need some sleep. It's only 1400 and I feel exhausted."

* * *

"!" Actus screamed as the biotic human bitch crush another bone in his foot. It felt like the bone had turned to powder.

"This is getting tiresome, Actus." Garrus said, from where he was leaning against the desk. Jack was enjoying herself immensely, if the huge, psychotic grin on her face was anything to go by. "Jack can keep doing this forever, even when we run out of bones, she can move onto more _sensitive_ places."

"Alright, ALRIGHT!" Actus gasped. "I'll talk, I'll talk, just make this crazy human bitch stop!"

"You have been talking, Actus." Garrus said grimly. He strode over to the chair the assassin was strapped into and leaned over him, gripping the arm rests tightly. "You told us who you are, what you do, what you like to do on off time, but not what I want to hear! Now who hired you?"

"I-I can't!" Actus whimpered. Garrus sighed and rolled his eyes. He pushed away from the weeping Turian. This was getting them nowhere and would soon degrade to just a beating rather than an interrogation Maybe he should switch tactics and-

"GURCK!" Actus shouted. Garrus blinked as Actus's left mandible was crushed by a biotic field.

"Jack!" Garrus snapped. Jack rolled her eyes.

"If he won't talk after that, he never will." Jack said smugly. Garrus glared at the biotic and was about to rip into her when Actus spoke.

"Shaco Vocker!" Actus gurgled with his broken mandible. Garrus face him in an instant.

"Where and when were you going to meet him for your pay?" Garrus demanded. Actus hacked wetly in pain.

"Vac ob Quah's Phirephlie woostewant. Wummaro, nibwight." Actus said broken. Garrus had to think for a moment before it click.

Quag's Firefly restaurant, tomorrow at midnight. Quag's Firefly was an old human ship retrofitted into a restaurant in a seedy part of Illium. It was open all hours and didn't ask questions.

"Thank you Actus. Jack, why don't you give our friend some fresh air?" Garrus said. Jack grinned happily.

"Love to!" She said in glee. She lifted the assassin with a biotic field and strolled over to the garbage disposal door. She hit the button to over ride it and opened the door exposing the long drop to Illium's ground.

"Happy landings, asshole!" Jack said cheerily and threw a screaming Actus out the door. Garrus smiled grimly in satisfaction. It may not have been what Shepard would have done but then again he had let Garrus kill Sidonis. He was sure the Commander wouldn't mind. Nodding to himself, he left to go tell the Commander and hopefully Liara the news.

They had a lead on the Shadow Broker.

* * *

To be continued…

* * *

A/N:

Review reponses:

Iverness: I hope I didn't disappoint!

Pico: And Elcor not being scary? Have you see this image? (just remove the spaces) = http:/ . com/ art/ MASS-EFFECT-2-Elcor-Spectre-128955389

Okay folks that's it for now! Look for an update in a couple of weeks! I'll try to keep to about a two week schedule but no promises.

See you later folks!

~Toby

v


	4. Chapter 4

**Title: **Mass Effect 3: The Reaper War

**Author:** Tobias

**Rating:** M for Mature

**Shepard Stats:** Paragon Shepard for ME1 & ME2. Romance is Liara T'Soni in both, Wrex lives, and the council was saved in ME1. The rest you'll learn as we go along.

**Author's Note:** I apologize for the wait on this chapter. But let me give you folks a tip. While I'm going to try and update it once a month I can't promise I will. I have to be in the mood to write and well, its been a stressful few of months. Just know I will never abandon this story. I hope you enjoy this chapter!

And by the by, I corrected a couple of things in the earlier chapters too. Makes it easier to follow. Might want to give them another read.

**Chapter 4**

When Garrus arrived at the infirmary, he found Miranda and Mordin standing over Shepard. He was lying on a medical bed next to Liara's and was deeply asleep. As he walked in they both looked up to see who it was. When they saw it was just him, they bent back to their work. Miranda was running a scanner over Shepard's left side as Mordin applied medi-gel on Shepard's minor wounds.

"I didn't think anything would get him away from Liara." Garrus observed as he leaned against Dr. Chakwas's desk to observe their work. Miranda didn't even look at him as she replied to his question.

"He was asleep in a chair holding her hand. I gave him a shot of something to keep him asleep for a bit so Mordin and I could patch him up." Miranda said, a bit smugly. Garrus rolled his eyes but didn't comment. He watched them work silently for a moment before moving to examine Shepard's armor. He gave it a once over, finding no serious damage before setting it back down. He turned around the two finishing up.

"How long will be be out?" Garrus inquired. Miranda wiped the sweat from her forehead before replying.

"About six or seven hours. I've repaired the damage to his servos and Mordin helped repair his ribs and elbow. We set the shoulder back in place a few minutes before you came back in. He needs to rest, the repairs to his servos was not minor and the nanites will take time to harden them. I'd say light duty for at least a week." Miranda said, shaking her head. Garrus sighed and clicked his mandibles.

"Must go, analyze nanite samples. Curious invention, yes most curious. Unlimited applications, but must test on DNA samples. Further analysis needed..." Mordin hurried out, taking a couple of vials of human blood, mostly likely Shepard's. Miranda and Garrus watched him go with amusement.

"Shepard may not heed that warning after he learns what we got from the assassin. He had a meeting with the Shadow Broker tomorrow at midnight." Garrus noted. Miranda sighed.

"I know Shepard cares a great deal for his people but what's the story between him and Dr. T'Soni?" Miranda inquired. Garrus blinked in shock, his mandibles dropping. Then he began to laugh.

"You mean in all your research on Shepard, Cerberus never even suspected that Shepard and Liara were intimate?" Garrus chuckled. Miranda blinked, taken aback.

"You're serious? We thought those were just rumors!" Miranda exclaimed. Garrus left the medical bay roaring with laughter as Miranda followed, demanding the full story.

* * *

Shepard awoke with a groan. His eyes fluttered open and he tried to sit up. His ribs ached and he clutched at them as he sat up. As his brain shook off the lethargy of a deep sleep he noticed he was no longer in the chair by Liara's bed. He was in shorts, tucked into a med-bed. He glanced around the room and saw Liara in the bed to his right. His armor laid out on the bed to his left and looked to be in good condition. He gingerly swung himself out of bed, noting the lights were dim, indicating it was the night shift. He shuffled over, each step gaining in strength. His left side felt better but taunt, like a pulled muscle. He slowly dressed himself, watching Liara's steady breathing as he did so. When he was done, he made his way to her to check on her vitals. Everything was in the green, and he smiled. He ran his hand over her head crest before planting a kiss on her forehead. Satisfied that she would be okay for a bit, he headed for the doors. As soon as they opened, he saw two crew men armed and standing watch, their backs to the med bay doors. They both turned as he walked out.

"Commander!" the crewmen on the right said surprised. They both saluted, and he returned it.

"What's the situation?" Shepard asked.

"Sir, Miranda asked for volunteers for guard duty. We have guards stationed here and at the Normandy's docking bay entrance in case another assassin tries to sneak on board. Garrus also wanted to speak with you as soon as you awoke, sir." the crewman on the left responded. Shepard nodded at them, heading for the elevator.

"Carry on." He replied. He entered the elevator and decided to start looking in the CIC. He found Garrus standing watch by the galaxy map. The Turian turned to see who was coming off the elevator and smiled when he saw the Commander.

"Shepard, trying to end up like me, are you?" Garrus said, stepping down. Shepard grinned.

"Have to send some of the women back your way, Garrus." Shepard said. "I heard about the guards. Think the Shadow Broker will try again?"

"Not right away, no." Garrus replied, shaking his head. "But Miranda wants to be safe rather than sorry. I do have some good news we got that from the assassin. He had a meeting with the Shadow Broker himself to collect his payment. Tomorrow night, midnight, at the Quag's Firefly." Shepard frowned, puzzled. He remembered what Wrex had said when he'd been working for the Shadow Broker.

"Doesn't that seem odd to you?" Shepard inquired. Garrus blinked.

"Now that you mention it, it does." Garrus said. "What do you think it means?"

"I don't know." Shepard replied. "But I'm going to find out. I'll be in my quarters, but do me a favor before you turn in. Send message to the teams, I want a meeting at noon."

* * *

The Elcor everyone knew as the Shadow Broker was waiting in a dark corner of the Firefly. He'd been waiting since a little before midnight and was becoming irritated. The Turian he'd hired to kill the T'Soni woman was late. It was already 00:23 and he was known for being punctual. The Shadow Broker had decided to leave when a Turian in dark blue armor sat down in front of him. It was scarred on the right side from a recent explosion. He was also wearing a helmet

"Shadow Broker." The Turian said curtly. The helmet distorted his voice.

"Annoyance: Actus, you are late. I had just been about to leave. For this insolence I will dock your pay ten percent." The Elcor rumbled. Actus shook his head.

"I don't care about the money." he replied curtly. "I was barely able to get away after I shot that Asari. Shepard damn near brought the shopping market down on us both chasing me."

"Suspicion: And yet here you sit, safe and sound." the Shadow Broker retorted.

"Barely." the Turian said, fingering the damage to his suit. "Now all I want is passage off this planet and away from that damned Spectre!"

"Shock: You are running away?"

* * *

"Keep him talking, Garrus." Shepard said into his comm device as he watched the meeting with the scope of his rifle. "Legion is tracking a comm signal to him from another location."

_"That's right, I want off this miserable planet _now_! Shepard will find me soon and you along with me if I stay here. And no amount of money can make me risk my own hide." _Garrus snapped, continuing to pretend to be Actus. The Shadow Broker was silent for a moment.

_"Acceptance: Very well but not expect to do business with me ever again."_

"Shepard Commander." Legion spoke up from Shepard's left. "I have located the origin of the signal. There is an empty apartment across the street from the restaurant with a perfect view of it and everyone inside. The signal is being broadcast from inside. Whoever is inside is listening to the conversation and talking tot he Shadow Broker."

"I knew it." Shepard said, turning his sights to the apartment Legion had indicated. "A decoy."

Shepard had suspected such, especially when he remembered something Wrex had mentioned in Chora's Den two years ago.

The Shadow Broker never did _anything_ face to face.

Now as he scoped in on the windows, he saw a shadowy figure watching from the windows. From the way it left hand was pressed to it's ear the figure was using a comm device.

"Legion, signal the others. Tell them to surround that apartment." Shepard ordered before speaking back into his comms again. "Garrus we located him! Keep the decoy talking as if nothing was wrong!"

* * *

Shepard swiftly and quietly moved up the hall, his shotgun at the ready. Legion was following him as Samara and Grunt moved down the opposite end. They positioned themselves around the apartment's door.

"Kasumi, Tali are you two ready?" Shepard asked over the comm. He had set them up just before the window on the ground floor.

"_Ready Shepard!" _Tali responded. Shepard nodded at Grunt.

"Break it down." Shepard ordered. Grunt smiled and stepped in front of the door.

"My pleasure, Shepard." Grunt snarled. He got a running start and barrel threw the door, sending shards everywhere. They stormed inside, quickly sweeping in. In the living room they found a burly Salarian snatching up a modified grenade launcher. Shepard snapped up his pistol, quickly firing. His round caught the Salarian in the hand and shoulder, and spun him around, knocking him to the floor a few feet from his weapon. The person by the windows slowly lowered his left hand from the left side of his head.

"Turn around, slowly." Shepard growled. He did so, stepping into the light as he did. It was a Turian, but he had no face markings at all and was dressed in very fine clothes.

"Shepard." The Turian said mildly. He glanced at the Salarian on the floor who now had Grunt's boot planted firmly on his chest. "Impressive how quickly you neutralized Tazzik."

"I take it that you're thereal Shadow Broker." Shepard growled. The Turian sighed and slowly moved to a recliner, easing himself down into it regally.

"I am." the Turian said loftily. "It's been a decade since anyone came even close. You and your Asari whore are to be commended."

"If I where you, I'd watch your mouth about her." Shepard snapped. The Turian shrugged.

"One of two things is about to happen, Shepard." The Shadow Broker said calmly. "You're either going to start working for me or you're going to kill me. And with what I could pay you, I think you'll find working for me is more beneficial Tazzik has outlived his usefulness and you could make a fine replacement."

"You son of bitch!" The Salarian snapped from under Grunt's foot. The Shadow Broker shrugged.

"I'm a realist, Tazz." he countered.

_"Shepard."_ Liara's voice came over the comm. Part of the plan Shepard and the others had worked up during the day included having Liara listen in during the mission. He suspected from the start it had been a ruse. He'd consulted Liara on how to approach it and she'd agreed to help only if she could listen in. _"Ask him about my friend, Feron. What happened to him?"_

"Liara had a friend, his name was Feron. What did you do with him?" Shepard demanded. The Shadow Broker waved his hand as if dismissing it.

"He betrayed me, so I made sure he paid for it. My Varren were hungry and he was good protein." he said dismissively Silence filled the room but Shepard heard Liara moan weakly over the comm.

"A wretch like you deserves to die." Samara declared. The Shadow Broker smiled.

"Yes, perhaps I do. But there will always be another Shadow Broker." the Turian said smugly. He stood up and walked to the windows. He stretched his arms out as if to embrace the night sky. "My family has been at this for centuries, Shepard. It's how the Shadow Broker has been here, working for years. When one dies, his son takes his place. When I die my son will do the same. So kill me, but the moment you do, you will be hunted by my son."

The Shadow Broker turned around to glare at them triumphantly Shepard quickly stepped forward and slammed the side of his gun against the Turian's face. Blood gushed out as he knocked the Shadow Broker to the ground.

"If I was a lesser man, I could just kill your son then." Shepard growled. He knelt down and poked the Turian in the side with his pistol. "You forget I have access to the council. I could take a DNA sample from you and track him down." Shepard stood.

"But I don't have to do that because I have a better plan." Shepard raised his Omni-tool and quickly stopped the recording. Then he uploaded it to the Normandy. "I've been recording everything you've said, and I'm going to send it to a good friend of mine. Ada Wong, reporter on the Citadel When she breaks this story it's going to be a matter of days before some one locates your family. And your sons will be very closely watched."

"You bastard!" The Shadow Broker roared, losing his cool for the first time.

"But Samara is right." Shepard said, aiming his gun at the prone Turian He quickly emptied the remaining clip into the Shadow Broker. "You don't deserve to live."

"What about his one, Shepard?" Grunt asked. Shepard turned to face the Salarian He shot the Spectre a panicked look.

"Tie him up and leave his for the police." Shepard said, heading for the door. "I'm sure they'd be interested to know who he is and what he was doing here."

"Shepard! Don't do this to me you filthy human!" Tazz screamed. He gave scream again as Grunt flicked him over with a bone breaking kick. When Grunt was done he walked out to join the others.

"Let's get back to the Normandy." Shepard ordered.

They quietly walked off as the sound of arriving police came from the elevator.

* * *

To be continued…

* * *

A/N: Ha! So how did you like the first arc? I know, its kind of short but still kind of fun, no?

Review reponses:

Pico: Yeah I had Garrus shoot Sidonis. But I also saved him in a different play through. It is interesting but I felt Garrus had more closure when he killed him.

Kudara: You assumed correctly! Did you like the conforntation?

Bandgsecurtiyaw: Thank you!

A reader: I know I tried to shave away from game mechanics a bit more this chapter. I hoped it worked!

Eden R. C. : Sorry about the wait! I hope you enjoyed it!

Garuda 1 Talisman: As a friend of mine loves to say, "It'll be done when it's done!"

See you later folks!

~Toby


	5. Chapter 5

**Title: **Mass Effect 3: The Reaper War

**Author:** Tobias

**Rating:** M for Mature

**Shepard Stats:** Paragon Shepard for ME1 & ME2. Romance is Liara T'Soni in both, Wrex lives, and the council was saved in ME1. The rest you'll learn as we go along.

**Author's Note:** Well, as I write this the Lair of The Shadow Broker DLC just came out in the past week. I played it, and while it was indeed VERY awesome it also basically knocks my plot on its ass and says "Fuck you!"

However my plot has now gotten up, brushed itself off and responded, "Fuck you bitch, I'm alternate universe!"

Yes that's right folks, this story is officially classified alternate universe. When did it happen? Well my Shadow Broker wasn't killed off by the DLC's Shadow Broker. Play the DLC to understand.

Now to the fanfic! Welcome to next story arc!

**Chapter 5**

"How are repairs going on the engine core?" Shepard asked. Miranda scanned her notes before responding.

"Engineer Donnelly says it will take another week to overhaul the energy couplings feeding into the main guns. Engineer Daniels is working with a crew to perform a detailed inspection and repair of the engines while in dry dock. Her crew has already replaced a few minor parts and repair minor stress wear. It will help stave off any major repairs down the road." Miranda replied. Shepard nodded before turning to Garrus. The Turian was leaning against the wall in the briefing room, waiting patiently.

"How are the weapons systems?" Shepard asked.

"They should be operational within the week. I also have a few more ideas I'd like to work into the Normandy during the final refit." Garrus replied, moving forward to set a data pad on the table. He slid it down to Shepard who caught it. "Two of them are purely defensive, but one might provide a bit of surprise for any pursuing Reapers."

Shepard quietly went threw the data pad, raising his eyebrows at the last weapon.

"That's illegal for most ships to carry, Garrus." Shepard replied, looking up from the pad. The Turian was smirking and clicked his mandibles before he spoke.

"Not for a Spectre's ship." He replied. Shepard couldn't help but grin a bit.

"Point taken." He replied, and he held out the data pad to Miranda. "See to it that these armaments are installed into the ship. Work with Garrus to make sure they are installed properly and _safely_. Last thing I want is for us to get hit with a warning shot and get blown to hell with our own stock."

"Yes Commander."

"Anything else we need to go over people?" Shepard asked. Everyone was silent in response and Shepard nodded, satisfied. In the three weeks since the incident with the Shadow Broker the crew had been perform admirably. Everyone had been working themselves to the bone since leave ended, and Shepard was pleased that most of the crew had returned.

"Dismissed. Tell all crews to stand down early tonight and get some rest. Ease a bit up on the repair schedule. I'd rather take a few extra days then have to go back over the work because of exhausted workers."

"Yes Commander." Miranda replied. The others bid him goodnight and left the briefing room. He reached out and touched the comm pad in the table.

"Joker, connect me to Councilor Anderson." Shepard ordered.

_"Yes, Commander. Patching you threw."_ Joker replied as the table sank down into the floor. Instead of the Illusive Man's quantum entanglement based communication array a holographic representation system like on the old Normandy had been installed. Shepard was surprised when not just Councilor Anderson appeared but the rest of Citadel council appeared as well.

"Councilors, I'm honored to speak with you. I'm sorry did I interrupt something?" Shepard said quietly.

_"Not at all Commander." _Councilor Rasila replied. She gave faint smile. _"We were speaking with Councilor Anderson when he received the notice of your incoming call. We wished to speak with you about recent events. We have just finished going over your report and we wanted to speak with you."_

_ "Indeed." _Councilor Inoste spoke up. _"I was very intrigued by the section that dealt with some of your crew members. A Geth, a tank bred Krogan, and even Mordin Solus? I knew him well we went to academy training, he was a excellent choice for a scientific advisor."_

"His dossier was very impressive Councilor. He is a excellent scientist and great friend to have. He does your race credit." Shepard replied. He hated playing politics but was not above telling the truth to grease the wheels.

_"If we can get to the matters we need to discuss?_" Councilor Actonite said, his mandibles twitching in amusement.

_"Yes, perhaps Councilor Anderson should start, he has the most distressing news out of all of us." _Councilor Rasila said, waving a hand at the man. Shepard couldn't help the spike of annoyance that shot threw him at he statement.

_"Thank you Councilor. Commander I'm pleased to see you survive the attack on the Collectors. I do have some distressing news from the Alliance. They have rescinded the death notices and announced that you are still alive. However, given your _disappearance_ for the past two years they have seen it as going AWOL. Also, being found to work with Cerberus has led they to declare you a traitor."_ Anderson informed him sadly.

"I'm sorry, what did you say? I've been declared AWOL and a traitor? That's absurd!" Shepard retorted.

"_We agree Commander." _Councilor Actonite replied._ "We spoke with your government and military officials. We went over your report with them in full detail, needless to say they have revoked both of those decisions."_

"Thank you Councilor." Shepard replied, feeling a bit numb. He blinked in shock when he heard the Turian councilor chuckle softly.

_"We may not always see eye to eye commander, but I do respect you and your ability to get the job done. I believe I speak for the Council when I say we will not let a Spectre such a yourself be thrown out of the airlock. Please continue Anderson."_

_ "Thank you Councilor. The Alliance has restored your rights to the mineral sites you had along with back pay, which comes to a very tidy sum. They have refused to restore your status in the Alliance military however. As of this moment your only allegiance is to the Council and the Spectres."_ Anderson informed him.

"Thank you Councilors." Shepard said gratefully.

_"We prefer it this way Commander." _Councilor Rasila said. _"We want our Spectres to have only one allegiance, to the Council. Others tend to confuse things."_

_ "As to the matter of these peace negoiations the Geth named Legion has asked you to mediate." _Councilor Inoste chimed in._ "We fully back this measure. We never agreed with the Quarians' decisions re-guarding their artificial race. In fact if they had handled it differently we might have known about the Reapers further in advance. You will help negotiate these peace talks Commander. Quickly however, we have much to do."_

"Sir?" Shepard replied puzzled.

_"The information that you retrieved from the Collector base was very illuminating Commander. It provides concrete proof, the Reapers are coming. We will stop them." _Councilor Actonite declared.

"Yes sir!" Shepard replied, grinning smugly.

_"We have much work to do until then Commander. We will begin rallying our forces and information will be leaked to the public slowly when we feel they can handle it. Right now as far as they know, an unknown race reprogrammed a portion of the Geth to attack us with Saren at the lead. They have just been informed that this was only the first wave. We intend to stop the second." _Councilor Actonite said firmly.

_"You will broker a firm cease fire between the Quarian's and Geth. Then you will have the Quarians mobilize the Flotilla for Citadel space. Their fleet must be refitted and reformatted for the upcoming conflict. You will also have the Geth spend a small portion of their fleet as well. The rest will be a relay jump away. We need them both to work on ways to stop the Reapers from deactivating the relays." _Councilor Rasila ordered.

"Yes ma'am. The Normandy will be finished in more than a week and I will start as soon as she's ready. Is that a problem?" Shepard asked.

"_No Commander. Proceed with your next mission and good luck."_ With that the signal cut out. Shepard couldn't help but grin broadly. He raised a fist in the air as the table rose and let out a scream of triumph.

The Council was finally on board.

* * *

"I got word you wanted to see me Mordin?" Shepard asked walking into the Salarian's lab. Mordin smiled, nodding rapidly.

"Shepard, excellent you could stop by. Have wondrous discovery to share! Need Council contacts to expedite distribution of findings." Mordin said excitedly. Shepard blinked, taken aback.

"Sure Mordin, anything I can do to help. What did you find out?" Shepard asked. The Salarian's smile widened.

"Obtained some of you nanites during your recent stay in the medical bay. Marvelous technology Cerberus has, most ingenious. Salarians attempted to create something similar but failed. Human nanites far superior to prototypes, adaptable, programmable Most impressive."

"Uh, Mordin, the point?" Shepard prodded.

"Yes, yes, yes the point. Nanites are incredibly small, almost the size of cell. Can be programmed to do numerous things. With Tali'Zorah's permission have obtained Quarian genetic samples and tissues. Have created a artificial immune system for Quarians, will be able to assist in recolonization of worlds. Wish to pass findings onto Quarian admiralty board and Citadel Council. Also presents solution to Krogan genophage issue. Possible alternative to genophage, can reduce vitality of Krogan population without causing still births." Mordin took a deep breath. "More research is needed on that issue."

"Mordin, that-that's incredible. You're sure this won't cause any long term affects?" Shepard inquired. Mordin nodded happily.

"Hundred percent sure. Installed fail safe programming into nanites. Un-hackable due to size and size of nanite colonies that will be inside subject's body. Single shot needed shortly after birth is all that will be required. Will also facilitate Quarian adaption. Within two, three generations tops Quarian will no longer need nanites." Mordin said confidently "Tali'Zorah has already agreed to be first live test subject should be arriving-" Mordin was cut off as the main doors to the lab opened. Tali walked in, wringing her hands nervously. "-now."

"Tali, are you sure your okay with doing this?"

"Shepard I've always dream of taking a deep breath of air without my suit's filters kicking in. If you trust Mordin then I will too." Tali said. Shepard gave her a long look before nodding.

"Do it but have full medical equipment standing by." Shepard ordered. Mordin waved a hand at a cart loaded with medical supplies with a chair by it.

"Fully equipped and ready for experiment Shepard. If Tali'Zorah is ready I will inject her using a injection port on her suit. When the nanites have spread completely threw her body she will then remove her helmet. If it does not work, we will notice an immediate reaction on her face. Her skin will break out in hives without antibiotics" Mordin informed them. Shepard frowned but Tali nodded in understanding. "Then we shall proceed."

"If this works Mordin," Shepard began as Tali moved to the chair, "I promise I'll help back you fully with Council and Admiralty board. After the meeting I had, I know the Council won't be much of a problem."

"Will work Shepard, I have full confidence in the science behind this." Mordin said, preparing a syringe filled with a thick gray fluid. He leaned down and adjusted a seal on Tali's left arm.

"Ready for the injection?" Mordin asked. Tali nodded.

"Do it." She replied. Mordin moved swiftly, injecting Tali and quickly depressing the plunger. Tali gasped and shivered. "It's cold!"

"Nanites and solution stored in medical cooler. Will adjust to your body temperature soon." Mordin said, taping away on his omni-tool. He was watching the readout carefully and after a few minutes nodded to himself. "Nanites are fully functional and have spread throughout Tali'Zorah's body. Please remove your helmet when you are ready."

"Moment of truth, wish me luck Shepard." Tali said, reaching up to the sides of her face plate.

"Luck Tali." Shepard said, watching anxiously. Tali undid the latches to her face mask and slowly pulled it off. Shepard got his first good look at the Quarian's face as he turned to look at him. Her face wasn't that mush different from a human's, with slight narrowing towards her chin. Her skin was a pale blue with dark blue lips. She had a cute little nose but her most prominent feature were her eyes. They were set and shaped like a human's but they were completely white, with no pupils what so ever. She took a deep breath and pushed her hood back to reveal the top of her helmet.

"Should I take off the rest?" She asked and without the speakers her voice sounded much the same.

"Not yet, but soon." Mordin replied. He was watching her carefully, keeping his omni-tool handy, consulting every thirty seconds or so. After five minutes Mordin smile satisfied.

"Nanites a success. Nanites have successfully blocked over three hundred benign bacteria and viruses common to human, salarian, turian and krogan as anticipated. I declare you perfectly fit to remove your suit." Mordin declare. Tali smile happily, removing the rest of her helmet. Shepard noted her hair was cut very short and was a dark purple in color.

"This is wonderful! Shepard may I have some credits, I'd like to go shopping! Oh things I'd love to see! I have to stop by one of Illium's boutiques for some things, then eat at this fabulous place I've heard Asari just brag about, and a park to catch the sunrise. Of and I so want to smell what a rose smells like and-"

"Whoa, whoa, whoa!" Shepard cut her off raising his hand. "Tali this is wonderful but we need to keep this under wraps for the time being. There are other Quarians on Illium and I know they would recognize what you are. You'd draw a hell of a lot of attention and we need to get the Admiralty board and the Council to sign off on this first, okay?"

"But Shepard-!" Tali protested.

"I know, its a lot to ask but we need to do this right. The Council wanted me to contact them anyways They want to back the peace treaty with the Geth. That's a good as time as any to give this to them too. It might even make it more attractive." Shepard replied. Tali winced but nodded anyways, her enthusiasm fading. Shepard sighed and shook his head.

"Look Liara moved her things into my quarters not too long ago. I know she'd love to see you and she'd be willing to loan you some things. Like battle armor for one thing. I'll Miranda and Kasumi get some things off ship for you too, and have Gardner whip his best meal us and the team tonight to celebrate, okay?"

"Okay!" Tali replied and got up from the chair with a bounce in her step. She quickly hugged Mordin who looked amused before doing the same to Shepard.

"Oh this is wonderful!" Tali cried and hurried out. Shepard watch her go and sighed.

"Mordin do me a favor, send your findings and the records of these results to the Council. I betting you know my Spectre coding so please use it to and mark the message urgent. I'll need to speak to them first thing tomorrow morning."

"Of course Shepard. Then I will prepare data for presentation to Quarian admiralty board and attend dinner. Much to celebrate oh yes!" The Salarian genius remarked hurrying out.

Shepard sighed and shook his head in amusement as he left the lab as well, intent on stopping the excited Quarian from attacking his recovering girlfriend in her excitement.

"Why do I get the feeling things just got more complicated around here?"

To be continued…

* * *

A/N: So what did you think? Not too shabby huh?

Review reponses:

Kudara: Arrogence sometime makes people stupid. Hope you liked this chapter!

Pico: I thought I worked well too. I was taken aback by who the real Broker was in the DLC though. Makes me wonder how many came before him.

Almostinsane: I'm trying to not use a beat. Help myself to go back and find the mistakes and typos. If you see any however after its publish feel free to point them out. I'll try to fix them!

Boom_Headshoot1377: Nothing on the Citadel. Yet. *~grins~*

Karen: I'm glad you liked it. Like I said, trying to work on the spelling errors.

Andrewjameswilliams: Thanks! I hope this was soon enough for you!

Grimreaper's Lost Soul: I will never rush this story. I ut off updating because I wanted to play the Shaodw Broker DLC to see how I could work it in. As it turns out I didn't need too.

Have a good night folks and don't worry, action and more to follow! This arc is just getting started!

~Toby


End file.
